Australia was told through ''intelligence channels'' that Australian Ben Zygier had been imprisoned in 2010 by Israeli authorities on ''serious offences'' under Israeli national security law, Foreign Minister Bob Carr has confirmed.

Mr Carr's comments come as Israel admitted for the first time that it held an Australian with dual citizenship under a false name for security reasons.

According to a statement on Wednesday from the Israel's Justice Ministry, Ben Zygier's Melbourne family was notified after he was detained. Zygier was reportedly known as ''prisoner X'' in the high-security jail.

Foreign Affairs Minister Senator Bob Carr at a Senate estimates hearing discussing the Australian man who died in an Israel prison in 2010. Photo: Alex Ellinghausen

Facing a Senate estimates committee on Thursday morning, Senator Carr said the Australian government was given assurances by Israel that Mr Zygier's rights would be respected.

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''The Australian government was informed in February 2010 through intelligence channels that the Israeli authorities had detained a dual Australian-Israeli citizen - and they provided the name of the citizen - in relation to serious offences under Israeli national security legislation. '' he said.

Senator Carr said the Australian government sought ''specific assurances'' from Israel that Mr Zygier's legal rights would be respected, that he would have legal representation of his choice, that his family would be told of his detention and that he would not be mistreated.

Ben Zygier.

''The Israeli government further advised the Australian government that the individual would be treated in accordance with his lawful rights as an Israeli citizen. The government relied on these assurances,'' he said.

Senator Carr said that at no stage during his detention did the government receive any request from Mr Zygier or his family for consular help.

He said that the government was advised - again through intelligence channels - on December 16 that Mr Zygier had died and that his family had been told. The embassy then helped with the repatriation of Mr Zygier's body.

''I speak with respect for the grieving of this man's family and I respect their grief at this news. And I hope that we can all of us discuss this matter . . . with that in mind,'' Senator Carr said

Foreign Affairs department secretary Peter Varghese told the committee that he did not know at this stage whether the foreign minister was told of the case.

Defence Minister Stephen Smith was foreign minister from February 2010 to September of that year, after which Kevin Rudd took over.

Israel's statement said Zygier was imprisoned according to a court order and that the prisoner's full rights were retained.

It says the prisoner was found dead in his cell two years ago, and that a judge ordered an investigation into his death.

About six weeks ago, the investigation concluded that he committed suicide.

However, a judge has asked the state to check for possible aspects of negligence.

Australia's ABC reported earlier this week that an Australian-Israeli citizen was held in secret by Israel and died in 2010 under mysterious circumstances.

In its report, the ABC named the prisoner as 34-year-old Ben Zygier, a Jewish lawyer from Melbourne who moved to Israel in 2001 where he was known as Ben Alon.

It said he was working for Mossad, and that his incarceration was one of the most sensitive secrets of Israel's intelligence community.